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- PDB-4mod: Structure of the MERS-CoV fusion core -

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Basic information

Entry
Database: PDB / ID: 4mod
TitleStructure of the MERS-CoV fusion core
ComponentsHR1 of S protein, LINKER, HR2 of S protein
KeywordsVIRAL PROTEIN / MERS-CoV / Viral envelope proteins / Spike / trimer of hairpins / 6-helix bundle / membrane fusion
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #300 / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Spike glycoprotein / Spike glycoprotein
Similarity search - Component
Biological speciesHuman betacoronavirus 2c EMC/2012
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsGao, J. / Lu, G. / Qi, J. / Li, Y. / Wu, Y. / Deng, Y. / Geng, H. / Xiao, H. / Tan, W. / Yan, J. / Gao, G.F.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of the fusion core and inhibition of fusion by a heptad repeat peptide derived from the S protein of Middle East respiratory syndrome coronavirus.
Authors: Gao, J. / Lu, G. / Qi, J. / Li, Y. / Wu, Y. / Deng, Y. / Geng, H. / Li, H. / Wang, Q. / Xiao, H. / Tan, W. / Yan, J. / Gao, G.F.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HR1 of S protein, LINKER, HR2 of S protein
B: HR1 of S protein, LINKER, HR2 of S protein


Theoretical massNumber of molelcules
Total (without water)27,8052
Polymers27,8052
Non-polymers00
Water2,324129
1
A: HR1 of S protein, LINKER, HR2 of S protein

A: HR1 of S protein, LINKER, HR2 of S protein

A: HR1 of S protein, LINKER, HR2 of S protein


Theoretical massNumber of molelcules
Total (without water)41,7083
Polymers41,7083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6980 Å2
ΔGint-64 kcal/mol
Surface area11090 Å2
MethodPISA
2
B: HR1 of S protein, LINKER, HR2 of S protein

B: HR1 of S protein, LINKER, HR2 of S protein

B: HR1 of S protein, LINKER, HR2 of S protein


Theoretical massNumber of molelcules
Total (without water)41,7083
Polymers41,7083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area7090 Å2
ΔGint-62 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.816, 42.816, 75.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-1301-

HOH

21B-1301-

HOH

31B-1354-

HOH

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Components

#1: Protein HR1 of S protein, LINKER, HR2 of S protein


Mass: 13902.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: amino acids 992-1054 (HR1) and amino acids 1252-1286 (HR2) linked by a 22-residue linker (LVPRGSGGSGGSGGLEVLFQGP)
Source: (gene. exp.) Human betacoronavirus 2c EMC/2012, (gene. exp.) synthetic construct (others)
Strain: HCoV-EMC / Gene: spike, S / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K0BRG7, UniProt: K9N5Q8*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS, 25%(w/v) Polyethylene glycol 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03906 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03906 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 12252 / Num. obs: 12172 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.442
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 11.717 / Num. unique all: 1267 / Rsym value: 0.156 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WNC

1wnc


Resolution: 1.901→37.783 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8258 / SU ML: 0.2 / σ(F): 2.04 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 583 4.79 %Random
Rwork0.1847 ---
obs0.1862 12169 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.4 Å2 / Biso mean: 21.5105 Å2 / Biso min: 2.84 Å2
Refinement stepCycle: LAST / Resolution: 1.901→37.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 0 129 1307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091210
X-RAY DIFFRACTIONf_angle_d1.0331638
X-RAY DIFFRACTIONf_chiral_restr0.071200
X-RAY DIFFRACTIONf_plane_restr0.003214
X-RAY DIFFRACTIONf_dihedral_angle_d19.3448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9009-2.09220.26251410.187629183059100
2.0922-2.39490.22571480.178429323080100
2.3949-3.01710.21651480.184428963044100
3.0171-37.79040.19521460.18692840298698
Refinement TLS params.Method: refined / Origin x: -8.1446 Å / Origin y: 10.6624 Å / Origin z: 18.0261 Å
111213212223313233
T0.0351 Å2-0.0037 Å2-0.0004 Å2-0.0314 Å20.0003 Å2--0.0413 Å2
L0.2027 °2-0.0954 °20.1419 °2-0.1198 °2-0.0909 °2--0.106 °2
S0.0077 Å °0.0007 Å °0.0129 Å °0.0011 Å °0.0203 Å °-0.0107 Å °-0.0385 Å °0.0143 Å °0.0072 Å °
Refinement TLS groupSelection details: ALL

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